Taverna Tutorial

Building a simple workflow

Stian Soiland-Reyes and Christian Brenninkmeijer

University of Manchester

materials by Katy Wolstencroft and Aleksandra Pawlik

http://orcid.org/0000-0001-9842-9718

http://orcid.org/0000-0002-2937-7819

http://orcid.org/0000-0002-1279-5133

http://orcid.org/0000-0001-8418-6735

Bonn University, 2014-09-01

http://www.taverna.org.uk/

This work is licensed under a

Creative Commons Attribution 3.0 Unported License

Available Service

We will start with something easy - retrieving a protein sequence from a remote database and identifying functional motifs

Expand the list

Available Services

Local Services

ncbi

Select ‘Get Protein FASTA’ and drag-and-drop it into the empty workflow diagram

Workflow input/output ports

In a blank space in the workflow diagram, Right-click and select Workflow input port from the Insert section

Type in a name for this input (e.g. ID) and click ok

Do the same to create a new Workflow Output Port. Call this output Sequence

Connecting ports

You now have 3 boxes in the diagram and we need to connect them up to build our workflow

Click on the input box ID and drag towards Get_Protein_Fasta and let go. An arrow will connect the two boxes.

Your first workflow

Click on the output box Sequence, drag towards “Get_protein_fasta”, and let go. An arrow will connect the two boxes.

You have now built your first workflow!

Running workflow

In the menu, select “File -> Run workflow”, or click on the green play button at the top of the workbench

Providing workflow inputs

An input window will appear. We have not yet added a description of the workflow or the input.

Click on ‘Set Value’ in the input window and add a Uniprot protein

identifier (e.g. P15409) where it says “some input data goes here”

Workflow results

Click Run workflow

The workbench changes to the Results perspective

In the bottom left, click onValue 1

You will now see a protein sequence from Uniprot

Validate your Workflow

Taverna can check to see that everything is connected properly and

that all the services in your workflow are available

Go to the workflow explorer (“Design” button) and click on

‘Validation report’ tab

See if Taverna has found any problems with the workflow. Errors will

be displayed in red, warnings in yellow. Workflows with warnings

often still run.

If there are problems, follow the instructions to resolve them by

clicking on the ‘Solution’ tab

Are you able to create a workflow that gives warnings or errors?

Tip: Try deleting the data link to the workflow output port